On 02/21/2013 05:44 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
Hi Conrad,
I'm sure that you are much better versed in and better positioned to chose than I. However, here are some thoughts:
First, is it critical that the mesh be triangular? Or can it be made of quads or n-gons? How important is the regularity of the mesh? A Voronoi surface implementation would be interesting, but it might present more difficulties than it is worth when trying to map bio/chem/physical properties to the surface.
VMD uses isosurfaces extracted from volumetric Gaussian density maps ("quicksurf") to create surfaces fast enough to be recalculated on the fly for animating trajectories.
I think that's what MOE does also. That's a wise choice.
This is similar to the tip that Elaine and Tom posted about "faking" a molecular surface when MSMS fails: http://www.ks.uiuc.edu/Research/vmd/current/ug/node72.html http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007048.html
The BioBlender project calls PyMOL for generation of its surfaces. As you know, PyMOL surfaces are distinctive and attractive, but not much faster than MSMS: http://bioblender.eu http://www.scivis.ifc.cnr.it/images/stories/PDFarticle/1009.4674.pdf http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06658.html
If I can vote, then I vote against Pymol's surface. It's just a hack, brute-force and inefficient algorithm (according to Waren Delano himself when you look into the subject on the net).
I like the spherical harmonics approach of Bruce Duncan, but I suspect that Chimera already incorporates this technique in the "Multiscale Models" module. http://mgl.scripps.edu/people/bsd/cv/cv.html
I wonder if "Surface Racer" could be implemented somehow. It seems very fast and it calculates per-residue surface areas, just like the current MSMS implementation: http://apps.phar.umich.edu/tsodikovlab/index_files/Page756.htm
OK, I'm tapped out for now...
Cheers, Darrell
Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH
31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public)
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On 2/20/13 12:24 PM, "Conrad Huang" <conrad@cgl.ucsf.edu> wrote:
We are starting work on Chimera 2, which will replace the aging user interface (Tk) and legacy graphics library calls (OpenGL 1 and 2). We will probably replace MSMS as part of that work.
We have examined a number of alternative algorithms, most of which do not compute analytical solutions as MSMS does. However, the numerical algorithms seem acceptable and are more efficient, so we will probably go with one of them. If there is a favorite molecular surface algorithm that you'd like to see in Chimera, please let us know (both which algorithm and why, which would greatly help us evaluate their relative strengths and weaknesses).
Conrad
On 2/19/13 6:10 PM, Francois Berenger wrote:
Hello,
Is there any plan to plug some alternative molecular surface calculation algorithm into chimera?
I have seen some interesting articles about isosurface and gaussian density functions:
"Yu, Z., Jacobson, M. P. and Friesner, R. A. (2006), What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. J. Comput. Chem., 27: 7289. doi: 10.1002/jcc.20307"
"What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules DOI: 10.1002/jcc.20307" http://onlinelibrary.wiley.com/doi/10.1002/jcc.20307/abstract
The algorithm looks simple, robust and even parallelizable. I kind of guess that's the algorithm used in MOE when I look at their triangulation.
Regards, Francois. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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